Aim.Measure the prevalence of human herpesvirus 6 (HHV-6) and cytomegalovirus (CMV) infections in children and adolescents with HIV infection and malignancy.Methods.Semiquantitative polymerase chain reaction and serology were used to test for HHV-6 and CMV infections in 31 cases (HIV-infected children with cancer), 56 HIV controls (HIV-infected children without cancer) and 30 cancer controls (HIV-uninfected children with cancer).Results.In cases, HIV controls and cancer controls, HHV-6 DNA was detected in 29, 39 and 34%, respectively, and CMV DNA was detected in 13, 4 and 7%, respectively. Four cases (13%) and no HIV controls or cancer controls harbored HHV-6 subtype A (P= 0.014). In cases, HIV controls and cancer controls, the prevalence of HHV-6 antibodies was 58, 68 and 93%, respectively, and the prevalence of CMV antibodies was 71, 48 and 70%, respectively. HHV-6 seroprevalence was lower in cases than in cancer controls (P= 0.002), even with adjustments for age and CD4 concentrations; however, HHV-6 infection rates (presence of HHV-6 DNA and/or HHV-6 antibodies) were similar in all groups. Stratification showed that CMV infection was more common in younger patients (ages < 8 years) without severe immune suppression (CD4 concentration >200 cells/&mgr;l) than in HIV controls (odds ration, 10.343; 95% confidence interval, 1.65, 121.57). Geometric mean titers of serum anti-CMV antibodies, but not anti-HHV-6 antibodies, were higher in cases (1:71) than in HIV controls (1:33) (P= 0.005).Conclusions.HHV-6 and CMV infections were common among children with HIV infection and cancer. CMV seropositivity also was associated with cancer in younger HIV-infected patients who did not have severe immune suppression. HHV-6A was detected only in HIV-infected children with cancer.